Neon Genesis Evangelion: Genesis Trilogy: Prophesy
by saberstorm
Summary: The Angels have been defeated. According to the Apocalypse Scrolls, Azrael is due to appear. The survival of humanity hangs in the balance, and Shinji is forced to choose. Life or Death? Impact or Instrumentality? Our only hope, may be our worst enemy.SR
1. Book of Lilith

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion. This story takes place after the initial storyline (after Koaru's death).

Author's Note: This is my redone version. I realized that I was going too wild with my idea, and I needed to calm it down or I'd end up in a mess. I will still keep the original up, but this is the real story. Most things will stay the same.

The Book of Lilith

Millions of years ago, the sun went into a stage of powerful flares. In a sudden burst of energy, a glob of plasma was ejected from the sun's surface. Surviving to reach beyond the corona, it supercooled in space, heading outward towards the planets.

It struck Earth about 65 million years ago, on the coast of the Yucatán Peninsula, exploding on impact. The impact ended the reign of the dinosaurs.

It was not the end of life on Earth. Rather, it was a new beginning. Inside the meteor, scattered across the globe by the explosion, were microscopic bacteria spawned by the intense furnace of the sun. These tiny bacteria joined to other organisms, jump starting the next stage of evolution for several species.

The Age of Mammals had begun.

Slowly, the Earth recovered. Its wounds healed. The world became green again, a shimmering emerald sapphire in space. As if by the will of a divine being, several of the remaining bacteria began to join together, forming cells, then tissue, then organs, then skin. A single being formed, a creature unlike anything else on Earth.

When the process was finished, the bacteria had spent their life creating more life, and the being that would come to be known as Lilith took her first breath.

The world was her garden, and she cared for it. She fashioned herself a two-pronged weapon to defend herself from the more dangerous creatures. When the first man walked upright and evolved to sentience, she taught him, like a mother would teach her child. She continued to watch over humanity as the years passed, feeling every birth and death due to her connection to the Earth's Geosphere. To stay hidden, she abandoned her true form for a more human form, burying her weapon in Antarctica, where she felt it would be safe. She watched as empires rose and fell, and realized that she needed her own correspondents in a world filled with greed.

When the UN was finally formed, so also did another, more secret group, SEELE. Their sworn obligation was to assist her in ensuring the survival of mankind and Earth. During the conflicts that followed World War I, SEELE manipulated the governments when they needed to in order to stop others from invoking Lilith's wrath. Though Lilith was unselfish and passive, she would not tolerate direct attacks on humanity, whom she considered her children.

In 1990, SEELE located several ancient documents of question near the Dead Sea. Calling them the Dead Sea Scrolls, they presented the writings to Lilith. She recognized them for what they really where, the Apocalypse Scrolls. Like the Necromancer and the Prophesies of Nostradamus, the Scrolls contained self fulfilling prophesies of the end of the world. Lilith warned SEELE that the Scrolls would never be applicable unless mankind acted on them, and requested that the Scrolls be sealed away.

One member, however, continued to study the Scrolls. His name was Adam Nagisa, the Japanese Representative.

In 1999, the Sun went into another storm. Another ball of ejected plasma streaked on it's course to Earth. This time, the magnetic field pulled the supercooled plasma toward the South Pole, causing it to land almost harmlessly. All the bacteria inside, except for a few in the very center, died in the cold Antarctic weather.

After being removed from SEELE, Adam worked in secret. He managed to extract and preserve the last of the bacteria, and began his experiments. He experimented on several creatures, saving his last for himself. When SEELE found out what he was doing, they sent the Katsuragi Expedition to stop him from finishing his final experiment.

Unfortunately, they failed, and the condition for the Apocalypse Scrolls was fulfilled. SEELE began working quickly to ensure that the fulfillment of the Apocalypse Scrolls worked to their end of allowing humanity to survive.

Thus the stage was set for the war between Man and God.


	2. Book of Asuka

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion. This story takes place after the initial storyline (after Koaru's death).

The Book of Asuka

_They all hate me. Let me die. I am no use anymore. Just let me die._

_'Now why would you want to do that, Frau Soryu?'_

_What the hell?_

_'Not 'what', but 'whom', Asuka Langley Soryu.'_

_Whom?_

_'Kaoru Nagisa, Nephilim, Fifth Child.'_

_Nephilim?_

_'Half Angel, to a small extent. The reason you can hear me know is because I am using my AT Field to connect our minds. Though I will admit that the fact that you forced yourself into coma helps.'_

_Angel?!?_

_'Easy! I am not an enemy. I am here to help you.'_

_Why? One of your kind raped my mind! Why do you think I placed myself in this coma?_

_'To answer your second question, I know it is because you don't want to face the memories you have buried. To answer your first, I want to help you because you are a fellow Nephilim.'_

_What do you mean? I don't have an AT Field._

_'Everyone does. It holds the Human body together. Nephilim and Angels, though, can project a second one using the Light of their Soul.'_

_So, every time I projected an AT Field while piloting Eva…?_

_'Correct. It was your AT Field. Unit 02 was made to help you control your powers.'_

_But I failed! The memories…_

_'Listen, Asuka, I cannot do this for much longer as using my AT Field causes my body to decay. My genetic structure is unstable because I am a partial clone of __Chairman Keil. After I do this, I will have to find a way to destroy my body so that I am not tied to it, allowing me to move to a new one. After that, I cannot help you, so please listen.__'_

_'You should not be troubled by your past. Your mother was ill because she was exposed to chemicals while constructing Unit 02 for you. But that does not mean that the man she loved, the one who you have every right to call 'father' is not evil. He has harmed many, and must be stopped.'_

_'So please put aside your anger, before he hurts more people.'_

_Who is he?_

_'You already know.'_

_No! It couldn't be!_

_'Unfortunately, yes. You are Shinji Ikari's half-sister.'_

_The Baka?_

_'Stay unconscious so that you can work through your feelings, please, or you could do something that could cause the death of many.'_

_O…K._

_'Tabrias, I cannot do this for much longer. Do you mind if I borrow Unit 02?'_

_………_

_'Tabrias?'_

_What did you call me?_

_'Tabrias. That is the name of the Angel of Alternatives.'_

_If it helps you, go ahead and use Unit 02._

_'I promise I will keep it safe for you.'_

_Wait! If I'm a Nephilim like you, and I'm Tabrias, who are you?_

_'I am your other. Call me Tabris, the Angel of Free Will.'_

HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

Kaoru spluttered and coughed up the LCL as he tried hard to keep from falling. He hated going through the transfer that put him into a new body, but it couldn't be helped since he was under constant threat of cellular breakdown.

"I see you made it back. You made contact with the Second Child?"

The Angel of Free Will smiled at the man who was handing him a towel. "Of course, Chairman Keil. I think she will return soon," he replied, accepting the towel.

"And the Third Child?" Keil asked.

At this question, Kaoru's face fell, "I believe he will be scarred emotionally by what I had to ask him to do. At least I gave him a good reason, so he should recover quickly, and be all the stronger for it." Keil handed him a pair of clothes and Kaoru began to dress, "I am more worried about my sister right now. It is obvious that she is in her third body, but Azela cannot seem to remember anything. I believe the old man is hampering her."

"We can correct that," Keil assured. "For a long time, I have been suspicious that the First Child was being abused by Gendo."

"Don't worry for now," Kaoru said, buttoning his shirt. "I believe Shinji-kun will be able to revive the memories of the Angel of Life."

"Do any of the three know of the true origins of the Angels?"

"No, nor should I explain it to them."

"The rest of SEELE will want a report."

"There are a few things I do not wish to tell them. First off, Yui Ikari is still alive. The AI core that she developed so the need for Nephilim as pilots would not be present is in Unit 01, and I could sense her soul was being protected by the AI."

"That would make sense. She programmed the AI to protect its pilots at all costs. That means the test was sabotaged, and it was forced to absorb her to protect her," Keil reasoned.

Kaoru nodded, "Yes, but that means she can still claim command of NERV, and I believe she is preparing to do that."

"All the better for us."

"There's more," Kaoru said, now grave. "The only reason the AI core would be used was if the pilot required it to keep his or her power in check."

Keil raised an eyebrow, "You don't mean…?

"We may have to accept that Shinji-kun is just who we feared he was: Azrael, the Angel of Death."

"Is he?" Keil asked.

Kaoru shrugged, "I don't know."

HHHHHHHHHHHHHHHHHHHHHHHHHHHHH

Gendo stood in the Eva cages, looking up at the masked face of Unit 01. "Soon," he said softly, "Soon it will be over, and there will be no more pain. We will be together, complete once more, Yui."

He turned to leave, only to hear a "ffttto" sound behind him as he was suddenly knocked to the ground by a clear, gooey, substance. He grumbled, muttering something about having just washed his suit, and turned back towards Unit 01. It remained as it was, still and silent. Idly wondering what had hit him and where it had come from, Gendo left.

HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

_**You sneezed on him?**_

**I think I have developed an allergy to his presence, Creator.**

_**Don't apologize! That was one of the most hilarious things I have seen in a long time, and he deserved it!**_

**When is the next test?**

_**It's nice that the MAGI don't tell anyone I can access them through the umbilical cable. The next test is tomorrow.**_

**Good. I wish to try to communicate with my pilot then.**

_**You need to be gentler with my son, Evan. **_(Author's Note: Pronounced A-van, as in Evangelion.) _**He's been through a great deal, more than anyone his age should have gone through.**_

**Indeed. He deserves your comfort. Therefore, if I can establish contact with him, I will try to help the two of you communicate.**

_**Don't absorb him, Evan. Not again.**_

**I have learned how to use the S2 I ingested. I am confident that we can reconstruct his body, should it happen again.**

_**I hope so.**_

**With where things are now, all we can do is hope.**


	3. First Book of Shinji

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion. This story takes place after the initial storyline (after Koaru's death).

The First Book of Shinji

Shinji Ikari was not a coward, at least not the kind he believed himself to be. His constant mantra, _I mustn't run away_, was his reaction to a natural instinct that kept him alive. His deepest desire was to start a new life, to leave behind the pains of the life he had now.

But his mantra held him back, and it was killing him.

It is natural to want to remove yourself from a situation that causes pain, and Shinji's life had been anything but pleasant. In spite of his self loathing belief, he was exceptionally strong, as a lesser man would have died already. That strength was easily evident to his mother, who saw it shining in his eyes when he was young.

When his mother was taken from him, that light began to dim. It was renewed briefly when his father promised him that she would come back. On that day, his father had given him a special drink, saying it was home made. On the following day, the sickness began. For two months, Shinji was terribly ill. He ran a fever, threw up constantly, and wet the bed several times because he was in too much pain to move. For the first two weeks of it, his father was kind and loving, caring for his son like any father should. But after two weeks his father changed.

"Stop throwing up!" he would yell angrily. "Be a man and hold it down!"

"Papa, it hurts!" Shinji would cry.

"Deal with it!"

After the sickness, the tests began: blood samples, urine samples, x-ray, CAT Scan, and even surgical exams. Shinji never knew what they were looking for, or why, and every time he asked, his father would slap him and tell him to not ask like the man he should be.

Whatever the results were, Shinji never found out. After a week of the tests, his belongings were packed and he was dropped off at the train station. His father turned and left, without even saying a word.

"Papa, no!" Shinji cried. "Come back, Papa! I'll be a good boy! Papa! PAPA!"

A year later, Shinji's uncle took him to see his father, walking right up to the elder Ikari's house. His father had simply said for his uncle to leave and never return.

"Papa! Why!"

His father's eyes showed no mercy as he looked directly at Shinji and said, "You are useless. I can't stand the sight of you."

"Where's Mama!" Shinji demanded. "You said you'd bring her back! You PROMISED!"

"Your mother is dead, Shinji," his father answered. "You saw it yourself."

"NOOOOOO!"

That one betrayal cut into Shinji's soul worse than anything else could. After that, it seemed that his fate was to have everyone betray or fail him. Once, he had a friend at school, who quickly became a bully when Shinji was unable to play sports well. Shinji ended up with a juvenile record after finding a bike someone else stole, and he was blamed for the crime since he was found in possession of it. His own aunt and uncle didn't believe him when he tried to explain that he had found it in the bushes near his school.

Even arriving in Tokyo 3 didn't stop the long list.

His father continued to prove he held no love for him.

Misato, who was like a second mother, began to fall into her own depression, and he began to doubt her words, as she would say one thing, and then the exact opposite, even when she was sober.

Asuka, his roommate who he thought he could always depend on for strength, in a coma.

Toji, his friend from school, he had heard nothing of since the 13th Angel. So far as Shinji knew, Toji was dead, and he was as guilty as if he had pointed a gun at his friend's head and pulled the trigger.

Kensuke, another friend from school that helped him keep piloting due to the nerd's envy, had moved away after the 16th Angel.

Hikari, the Class Rep, he couldn't look in the eye since the 13th Angel, and even then, they had never really talked. He didn't really know anyone else in his class either.

Rei Ayanami, a girl he knew he had a crush on, and maybe even loved, had died during the 16th Angel. He was told she had survived, but when he saw her, he knew it wasn't the Rei who seemed to understand him the most. Then he had seen the horrors in the Room of Gauf, and learned that Rei might be a clone of his own mother, and that the other clones in the Room were her replacements, should she die.

The last, and worst, had been Koaru Nagisa. He listened to Shinji like no one else. He was like the brother Shinji never had. Granted, he was weird in several ways, but Shinji thought that was because Koaru had never had a family.

Killing Koaru had been the final straw for Shinji. His mind had broken, and his soul was shattered. Images of what had been, what could have been, what was, and what could be ran through his mind in no apparent order. The night after he killed Koaru, as he lay in bed, he finally fell over the brink into insanity. His body lay on the bed, unmoving as his awareness became nothing more than a small, dark corner inside his mind. His body continued to function as if nothing was wrong, but it never moved.

Deep inside his blood stream, a small, microscopic organism that had lain dormant after his body tried to reject it could finally begin its work. It latched on to the nearest cell, taking apart and reconstructing the DNA inside, and then moved on to the next one. Every altered cell began altering the ones next to it, and so on.

Shinji's transformation had begun.


	4. Second Book of Shinji

Evangelion: Prophecy

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion. This story takes place after the initial storyline (after Koaru's death).

The Second Book of Shinji

Misato awoke early, something she normally didn't do. Today was different though. In the past week since the 17th Angel was destroyed, she had started drinking less, and going to work more. Every morning, she checked on her ward, Shinji, hoping to see some improvement. Each morning was the same, as was the evening when she came home, and it broke her heart.

For the entire week, he did nothing, said nothing, and ate nothing, just laid in bed listening to his SDAT. Nothing his guardian, Misato, did could make him acknowledge him. He wanted to die. But it wasn't his death wish that worried Misato.

It was the fact that he should already be dead. In spite of having not slept, eaten, or even moved for a week, he was still alive.

This was why she was going to work early today. The day before, Ritsuko had been released from the brig at NERV. Misato hoped she'd know what was wrong.

HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

"No idea?" the purple-haired Major asked again.

"None," the doctor replied, sullen.

Misato sighed. It was obvious that she wasn't going to get any answers from the fake-blond. She left NERV and headed back to the apartment. _Shinji's friends should be coming back tomorrow_, she mused. _Maybe they can snap him out of it_.

Entering her apartment, she was surprised to see it was cleaner than when she left. It wasn't perfect, but it made her wonder. "Nice to see you got up, Shinji!" she called happily, opening the door to her charge's room. Shinji was still lying in bed, unmoved from when she had last seen him. What surprised her though was the girl with blue hair sitting nearby, watching him.

"What are you doing here, Rei?" Misato asked.

The First Child turned toward her, "I came to see Pilot Ikari, Major. I have not seen him report to NERV and wondered if he was ill."

"I wish I knew, Rei," Misato said, leaving for the kitchen to get a beer. Ever since Ritsko had shown her and Shinji the Dummy Plug System, the Major had always felt uncomfortable around the red eyed clone. _Though I wonder who she was cloned from_, she thought yet again.

Back in Shinji's room, Rei decided to try to wake up her fellow pilot. She reached out and touched his hand.

_"I'm not sure what to do in this type of situation."_

_"Why don't you try smiling?"_

_Reaching out to take his hand, feeling warm, smiling…_

Rei snapped back to the present and sat back, confused. It had happened again. Ever since she had used her AT Field to help Shinji stop Kaoru, she had been experiencing strange memories and feelings. Most were associated to times when she thought of the dark-haired pilot in front of her. _He reminds me of something. No, someone. Who? Who?_

_"I'm scarred."_

_"Its okay, Rei, I don't think he'll hate you. Those wings actually look quite beautiful."_

_"But…"_

_"Those wings are a good thing. It means your body is stable enough to handle your AT Field. You won't suffer from cellular breakdown anymore."_

Again, Rei snapped back to the present. That last memory had been even fuzzier than any of the others. It was like it was from so long ago, that she could hardly remember it. _I should ask the Commander about this_, she thought, and rose to leave.

She was unaware of the battle that was currently raging inside the poor boy's mind.

HHHHHHHHHHHHHHHHHHHHHHH

_"What is this?"_

_"This is the result of your father's work," Misato said. "This is Instrumentality."_

HHHHHHHHHHHHHHHHHHHHHHH

For the first time to her knowledge, Rei was afraid of being in the Commander's presence. She had reported these 'flashback' moments, and was surprised to see him suddenly rise and question her about them as if she were a criminal. Aparently, she had answered his questions to his satisfaction as he had calmed down and sat back in his seat. His hands were folded in front of his face, showing he was thinking deaply.

She remained were she was, at attention. She took another breath, and saw the puff of carbon dioxide that told her just how cold it was in the Commander's office. Her skin had already gone numb from it, and she wondered if she'd get frostbite if she stood here for much longer.

Finally, he answered her. "Pay no heed to it, Rei. It is just a side affect from your activation."

Rei bowed politely, "Thank you, Commander." She turned and left the gloomy office.

"Are you sure it was wise to tell her that, Ikari?"

"I cannot afford to have her develop a will of her own yet again."

HHHHHHHHHHHHHHHHHHHHHHHH

_Red skies, red sea, desolation, destruction, sadness._

_"How disgusting."_

The vision vanished.

_'That ending again? No! Reanalyze. Show me another possibility.'_

The vision began to open again, showing another possible outcome. Not everyone knew it, but Tabrias had also read the Dead Sea Scrolls when she was a child. She didn't remember much, but it was enough to predict the outcome.

_'This is why he called me the Angel of Alternatives. I can predict Alternatives. If I concentrate hard enough, I can look at the world around me, what others do, how they react, and predict their moves. I used to do that in the Eva simulator training in Germany. I did it in college, which was how I could graduate. The reason why I haven't been able to do so recently is because I lost my focus. There has to be more.'_

_Gendo laughing. Third Impact. "How disgusting."_

_'Damnit!'_

HHHHHHHHHHHHHHHHHHHHHHHHH

The doctor watched the monitor with interest. One week ago, the Second Child's brainwaves had been spiking. She seemed to be undergoing one continuous lucid dream that was repeating itself over and over. The doctor looked at the pilot's face, noting the signs of REM sleep, made a note on his clipboard, and left to write his report.

Had he paid more attention, he would have noticed the faint blue-wave pattern on the screen.

HHHHHHHHHHHHHHHHHHHHHHHHH

_I guess…_

What?

_I don't have to pilot the Eva, if I want to be happy._

Won't others die?

_Yes. I can still pilot Eva. But I don't need my father's approval to be happy. I have the approval of others, and not just with Eva. There's school, there's other hobbies I have…_

So what will you do instead?

_My cello. I've always been good at it. I'll try out at places._

What if they don't like you?

_There are other places._

So?

_So I always have another option, another choice._

Yes!

_He was standing now, standing above the world. Everyone he knew was applauding him. He took a bow. "Thank you, everyone."_

_Everyone else vanished, and he saw a single being. It was a woman, covered in white armor that resembled an Eva. An S2 core pulsed in her abdomen. Her head was topped with blue hair that had streaks of silver, and her bangs hung down into her red eyes. She hovered in front of him with feathery wings of gold, approval on her smiling face, as she nodded and spoke._

Yes, that is correct.

Take care of yourself.

HHHHHHHHHHHHHHHHHHHHHHHHHH

Shinji opened his eyes, and for the first time in a long time, he smiled. "I will," he promised. He didn't know who he was promising, but he knew that he was at least making that promise to himself.

_I will not run away from what happiness I can find anymore_, he thought. Then he dragged his stiff body out of his bed and headed for the bathroom.


	5. The Acts of Traitors

Evangelion: Prophecy

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion.

The Acts of Traitors

Misato sat down once more at her laptop, inserting the thumb drive that Kaji had given her before he died. She had not looked in it for a while, unable to understand what she was reading. However, now, she thought she might be able to figure it out. Slowly, she gathered her courage and clicked on a file labeled _To my Sweetheart_.

_Dear Misato,_

_By the time you read this, I may be dead. I have, unfortunately, betrayed a few too many people to really escape such a fate for much longer. The files contained in this drive hold everything I've learned about NERV and Commander Ikari's deceptions._

_There are some things you have to realize you won't understand right away. You'll have to talk to people at the right times to fill in some of the holes. Even I don't understand everything I found, but SEELE will. Commander Ikari should have shown you some of this stuff a long time ago, but he has kept it hidden from __Everyone__, including Ritsuko, Rei, Shinji, and maybe even the Sub-commander. Worse, SEELE doesn't know that he's stabbing everyone in the back. If Commander Ikari isn't stopped, I fear it will already be too late to save humanity._

_I need you to get my report to SEELE. I don't know how to help you do it, but I need you to do so._

_Letting go of you was the worst mistake of my life. If I had not been such a coward, I think things would have turned out differently. I hope Shinji doesn't make the same mistake I did._

_Above all, Misato, please remember this: I love you._

_-Kaji_

That was as far as she had gotten last time. After that, she couldn't bear reading any more. Now, however, her curiosity had gotten the better of her. She needed to know.

She noticed a folder labeled _Katsuragi Expedition_. She opened it to see several report files, and something labeled _To my Daughter_. Misato clicked on this first.

_Misato-chan,_

_I am sorry for the pain I have caused you. I have left this letter with those I trust in hopes that should the worst happen, you will be able to receive this._

_You see, Misato, I am the Japanese representative of an international organization called SEELE, who's goal is to preserve mankind. If we cannot stop Adam here, in Antarctica, where he is vulnerable, we will be forced to fight against a being with the power of a god._

_No mortal should have the powers Adam now has, he stole them._

_It all leads back to Super Solenoid Theory. Have you ever wondered how, someone so small at birth can become so large as an adult? The answer is in S2 Theory. Ingested food is converted into energy, and then back into tissue; matter, to energy, to matter. This process is heavily assisted by blue blood cells. Just like the name suggests, they are like red blood cells, only blue instead of red. So why can't we detect them? Why is our blood red instead of purple. That is because blue blood cells are nanocells, and the average human only has one blue blood cell for every 10,000 red blood cells. However, in spite of their small size and small number, these cells are incredibly powerful, and can change the evolution of mankind._

_In fact, the author of the Necromancer, the man known as Nostradamus, and the author of what we at SEELE refer to as the Dead Sea Scrolls (Not the same ones that form part of the Bible) were more than man. They were nephilim. They had a 50 percent concentration of blue blood cells; that is, one blue blood cell for every two red blood cells. That is the minimum amount required to project the Light of the Soul, or what we refer to as the Absolute Terror Field._

_You see, the power of a human soul is incredible. Without our blue blood cells, our bodies would fall apart as primordial mush under the strain. Our blue blood cells hold our bodies together, and the energy they use is an AT Field. However, someone with a 50 percent BBC count has enough energy to project it outwards in various ways, defensively, or offensively. Some can even distort time and see future possibilities. Those who can do this and remain human are called nephilim, because they have the ability to fly. Whether they have wings, I cannot say. I am only repeating what I have been told._

_Adam Nagisa, my predecessor, sought such power and more. He was removed from SEELE, but he has experimented here in Antarctica with bacteria that are known to generate blue blood cells. That is why we came here, only to find we were probably too late. He has already created several monsters through his experiments. I'm not sure, but I'm certain some were once a bear, a lobster, a starfish, a hawk, an eagle, an ant (probably a queen, if we are reading his records right), a spider, and worst of all, his own unborn children, causing their mother to die early. Poor Thing! We managed to save the children though, but the hardships they face will be terrible._

_His last experiment was on himself, turning himself into a monstrosity. His BBC count is 200 for every red blood cell, enough power to destroy this world, and use humanity as his toy. We know because a 100 percent BBC count (one blue blood cell for every red blood cell) has so much energy that it sends out a wave pattern that we can detect through radar._

_I only know he must be stopped. I will do my hardest, my daughter. I will do it for you, for your mother, for anyone you may meet. I may fail, but I hope that if I do, I will not have died in vain, for I will have provided the information necessary to stop him._

_Live well, my Misato-chan, and know that through all I did to you, all I wanted was to keep your future safe. If I failed, I hope you can forgive me for that too._

_-Your Father, Captain Katsuragi_

Misato closed the laptop as tears began to run down her face. She had never known. A lot of things suddenly made sense now. Why had the Commander hidden this from her? So she could live in her hatred? He was manipulating her for certain. He was manipulating and lying to everyone. She wasn't going to let Kaji down. If SEELE could answer some unanswered questions and stop the Commander, then she was behind them. She powered down her laptop, and headed into the kitchen to grab a beer when she saw a sight that warmed her heart.

"Oh! Hi, Misato! Would you like something to eat?" Shinji asked.

HHHHHHHHHHHHHHHHHHHHHHH

_Augh! Why can't I do this?_

You're going about it the completely wrong direction.

_What the…? Tabris?_

No, Tabrias. I am Lilith.

_You're who?_

I suppose you could call me Tabris' mother.

_Right. I'll believe that when I see the two of you. And what do you mean that I'm doing it all wrong?_

You're trying to force your own observations a beliefs on your visions. It doesn't work that way. Things are not always the way you preserve them.

_What do you mean?_

How about an example? I happen to know Shinji better than you do, even though neither of you know it. One thing he would never do is what you see him doing at the beginning of your vision.

_Do you mean…?_

Yes. I mean, come on! He's not like his father!

_He's a pervert._

That's what you think. Have you ever given thought that maybe he just wanted a friend, that maybe he saw you as the sister he never had?

_Ironic, seeing that I am the Baka's sister._

There's no need to be so grouchy about it.

_He's a Pervert!_

You're just mad because you had a crush on him. But wait! That would make you the pervert, not him, now wouldn't it?

_…………_

Oh, I'm sorry. Did I hit a nerve?

_You want a pick a fight with me?_

I'm sure we'll both enjoy it. After all, you've spent all your life training for a fight, and I could use some mental exercise.

_Wait! Mental?_

Time to see if you learned anything when the 15th attacked you.

HHHHHHHHHHHHHHHHHHHH

"Well, Shinji, that was a feast!" Misato said.

"Thanks," Shinji replied, clearing the table. As soon as his arms were empty though, he felt himself get pulled into a hug.

"I missed you, tough guy," Misato told him. "Having you out like that all week was hard. I couldn't do anything to make you get up, but I was too scared to call the hospital and have them take you away."

"It's okay," Shinji told her, returning her hug. "You needed me, just like you needed Kaji."

Misato stiffened, "How'd you know?"

Shinji himself paused, "I had a weird dream while I was out. It was like I was seeing things from inside the minds of those I knew; how they saw me, and why they saw me that way. But I also saw more than that, but I didn't think it was real."

_That night, that night when I dreamt that I was being judged, did he see it? Was he really there? And why?_ These questions ran through Misato's head before the phone interrupted her thoughts.

"Misato, come quick!" came Ritsuko's panicked voice from the other end. "Asuka's having a seizure, and she's giving off a blue pattern!"


	6. Book of Kyoko

Neon Genesis Evangelion: Genesis Trilogy: Prophecy

Summary: The Dead Sea Scrolls predicted 4 Nephilim: Tabris, Tabrias, Azela, and Azrael. They would protect humanity against the Angels. But in order to do so, one would destroy everyone. Is Shinji Ikari really Azrael, the Angel of Death? And what exactly is Instrumentality? How does it differ from Third Impact?

Disclaimer: I don't own Evangelion. This story takes place after the initial storyline (after Koaru's death).

* * *

Book of Kyoko

A fist landed next to Misato's eye, stunning her momentarily and allowing the red-haired girl to escape her grasp as she continued to flail about. She was spared another strike from Asuka by Ritsuko's quick hand, but together they still couldn't restrain her. Still, they persisted, trying to stop Asuka from hurting herself as her body shook uncontrollably. Unfortunately, the more they struggled to hold her down, the more she fought against them.

Finally, they were both blown backward as an AT Field manifested itself in a cocoon shape around Asuka, who curled up in a ball and didn't move.

Misato turned to Ritsuko, "Any ideas as to what is going on?"

Ritsuko shook her head as she stared at the Field. Shinji approached causiously, lightly placing his hand on the glowing boundary.

"Asuka?"

HHHHHHHHHHHHHHHHHH

Asuka…

Wake up, Asuka…

_Go Away! I don't want to see anymore!_

You can't keep running away from your problems like this, Asuka.

_So shoving them down my throat is supposed to help?_

The answers to your problems are in your memories.

_I Don't Want To See Them! Stop Showing Them To Me!_

Then you'll never move on. Don't you want to know the truth?

… … …

Well?

… _Yes. I do._

Then I will use my powers to enhance your memory, and show you.

HHHHHHHHHHHHHHHHHH

To Asuka, it was as if her life was playing backwards on a tape. She saw her worst memories flash before her eyes, including being strangled by her mother. But as she continued to go backwards, she noticed something.

_Who are they?_

The image froze as she looked at that particular memory. She could see her mother, still healthy, talking to an older woman who had a small boy and girl hiding behind her leg. There was also a very old man there, who had another small boy standing next to him with an odd smile. Their names came to her instantly.

_Mama, Yui, Shinji, Rei, Keil, Kaoru._

_I knew them. I knew them all._

Now the memories started to move forward. She saw herself playing with the other children, being watched by a woman who had blue hair streaked with silver. She saw a sweet memory when she fell and skinned her knee, and Kaoru stayed with her in the Nurse's Office until she felt better.

_I forgot all about them, because I didn't want to remember what happened to Mama. I pushed all my memories back._

She saw more memories play before her. Her constant teasing Shinji and Rei. Listening in on the Adults as they talked behind closed doors using a cup against the wall. Trying to teach Rei to play with dolls.

_Wait! I liked dolls?_

Making a doll of herself, and giving it to her mother.

_So that's where she got it._

Sneaking into her mother's lab and stealing a vial of something. Running away and hearing footsteps behind her. Panicking and thinking she was caught. Swallowing the fluid and throwing the vial away to try and remove all evidence. Becoming sick for several weeks and being hospitalized.

_That was stupid of me_.

Then, one final memory flashed before her.

HHHHHHHHHHHHHHHHH

A three year old Asuka crouched next to the door, placing the cup against the wall to hear inside the room.

"How does it look."

"Not good, Kyoko. I'm sorry."

"How bad is it, Yui?"

"Mental Degeneration. It's genetic, but with the chemicals you were exposed to, you probably won't last another two years. I'm really sorry, Kyoko. Not even Gendo would want you stuck in here for the rest of your life."

"What's going to happen between the two of you?"

There was silence before Yui answered, "I filed for divorce."

Asuka heard her mother gasp, "Oh no! Yui, don't do that just because of me!"

"It's not just that."

"Don't say that! I know I was married to him and distraught over his divorcing me to marry you, but that's no reason to…"

"I caught him cheating on me."

Another gasp, "With who?"

"Nao."

"No!"

"Yes. It's not enough that I gave birth, he still has to be 'satisfied', and because I'm not around to do it, he gets someone else."

"And to think I asked him for his genetics for my child. What have I done to my poor Asuka?"

"Don't worry, Kyoko. Everything will work out."

"And if my Mental Degeneration is genetic, what will happen to her."

"She won't suffer from it, since she stole the sample and ingested it."

"Which means she'll have to pilot it?"

"Most likely."

"What about your AI experiment?"

"Keil says that even if it doesn't work, he still wants it installed on every Eva. But the one that will be in Unit 01 will be the most powerful."

"Will it work though, so that older people can pilot them?"

"I don't know. I hope so, but the Scrolls say that only Nephilim will fight."

"Not my Asuka. She'll be going through enough pain as it is!"

"I don't want her fighting any more than you."

"By the way, do we know anything about the stolen sample?"

"Nothing, though I think Gendo has it."

"He's been searched three times!"

"I know which makes me dislike him all the more. He's hiding something, and whatever it is, I don't like it."

At that moment, Asuka sneezed, and the adults paused. Then her mother said, "That could be Asuka listening in again."

"I'll look."

Asuka quickly dashed down the hall and around the corner. The last thing she really wanted to do was be caught by Yui Ikari.

HHHHHHHHHHHHHHHHHHH

_Now things make sense! Things are not always what they seem to be! I need to look at all the possibilities together! That's why I couldn't get beyond that first possibility!_

So she tried again. This time, it was different. A massive, white giant hovered in a red sky, a red sea beneath him. Massive wings of energy spread from his back, radiating power that bordered on absolute.

Then one, two, four, five Eva's appeared, each with wings of their own, circling the massive giant. She saw her Unit 02 open its mouth and speak:

"Oh filthy hypocrite, he who tried to be a god incarnate, how low you have fallen. All your abominations destroyed, and none to defend you. Here and now it shall be decided, and we shall triumph and restore humanity. You can't cause a Fourth Impact, and your attempt at a Third failed. Now you shall finally pay the price for your Second Impact, Adam."

The giant growled, and the battle was joined.

And the vision vanished.

HHHHHHHHHHHHHHHHHHH

"Asuka?" Shinji asked again, hoping to get through to his roommate. Asuka's eyes slowly opened as large, white feathered wings unfurled from her back. She smiled standing as her AT Field dissipated, now completely under her control. Her eyes lost focus, and she teetered. Thinking quickly, Shinji caught her before she could fall, and was surprised to feel her embracing him with her arms and her new wings.

"Thank you, little brother," she whispered, before promptly falling asleep.

HHHHHHHHHHHHHHHHHHH

Rei Ayanami continued to stare at the ceiling of her apartment. There was nothing else for her to do for now. Her homework was done, and she had no duties at NERV for the time being.

"I am not needed," she thought aloud.

_I would not simply assume that, my child._

She sat up in shock, "Who's there?"

_You know who I am. Listen carefully…_


End file.
